[Mrtrix-discussion] Urgent global tractography

[Vinay Kumar Shukla]

Hello Everyone!!

I converted dicom data using mrconvert.
vips at Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$ mrinfo dwi.mif 
************************************************
Image:               "dwi.mif"
************************************************
  Format:            MRtrix
  Dimensions:        768 x 96 x 34
  Voxel size:        2.20833 x 2.20833 x 3
  Dimension labels:  0. left->right (mm)
                     1. posterior->anterior (mm)
                     2. inferior->superior (mm)
  Data type:         32 bit float (little endian)
  Data layout:       [ -0 +1 +2 ]
  Data scaling:      offset = 0, multiplier = 1
  Comments:          3T 2D EP TR=6000ms/TE=136ms/FA=90deg 20-Jan-2009 13:8:25.938 Mosaic
  Transform:                    1           0           0      -103.8
                               -0           1           0      -81.99
                               -0           0           1       -38.2
                                0           0           0           1

but when I used dwi2tensor it says 

vips at Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$ dwi2tensor dwi.mif dt.mif
dwi2tensor: dwi image should contain at least 4 dimensions

Can any body help me out what went wrong.

looking forward for reply

kind regards
vinay

----- Messaggio originale -----
Da: "Thijs Dhollander" <thijs.dhollander at gmail.com>
A: "MRtrix discussion" <mrtrix-discussion at www.nitrc.org>
Inviato: Mercoledì, 26 marzo 2014 17:46:05
Oggetto: Re: [Mrtrix-discussion] Urgent global tractography





Hi Vinay, 

I'm not 100% sure, but I suppose you might have been confusing the term "global tractography" with "whole-brain tractography"; is that correct? 

If so, a good step-by-step tutorial on doing (whole-brain) tractography using MRtrix is provided in the manual: http://www.brain.org.au/software/mrtrix/tractography/index.html 




An detailed overview on the parameters/choices offered by MRtrix, and their impact on the final result is provided in the following paper: http://onlinelibrary.wiley.com/doi/10.1002/ima.22005/full 


Hope this helps! :-) 


Cheers, 
Thijs 



Thijs Dhollander 
thijs.dhollander at gmail.com 
Tel. +32 475 36 44 27 
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven 


On Wed, Mar 26, 2014 at 5:05 PM, Vinay Kumar Shukla < vinaykumar.shukla at univr.it > wrote: 


Dear Daan, 
thanks for your kind reply and update. 
I mean steps need to follow to do tractography 
using Mrtrix. Because I look at documentaion 
and bit confuse from to start. I have DW data sets and grad file in text. 
What should I do and how to process it using mrtirx. 
any help would be really grateful. 
kind regards 
vinay 

----- Messaggio originale ----- 
Da: "Daan Christiaens" < Daan.Christiaens at esat.kuleuven.be > 
A: "Vinay Kumar Shukla" < vinaykumar.shukla at univr.it >, mrtrix-discussion at www.nitrc.org 
Inviato: Mercoledì, 26 marzo 2014 16:58:12 
Oggetto: Re: [Mrtrix-discussion] Urgent global tractography 

Dear Vinay, 

MRtrix does not offer global tractography for the moment. I¹m developing 
an add-on for this, but it¹s not yet ready to share. In the mean time, 
check out MITK Diffusion ( http://www.mitk.org/DiffusionImaging ). 

Best regards, 

Daan 


ir. Daan Christiaens 
Ph.D. Researcher 

<mailto: daan.christiaens at uzleuven.be > daan.christiaens at esat.kuleuven.be 
tel +32 16 34 90 35 
fax +32 16 34 90 01 

Medical Image Computing ­ ESAT/PSI ­ Department of Electrical Engineering 

Medical Imaging Research Center < http://www.medicalimagingcenter.be/ > | 
Katholieke Universiteit Leuven < http://www.kuleuven.be/ > | campus 
Gasthuisberg < http://www.uzleuven.be/ > | Herestraat 49 bus 7003 | B - 3000 
Leuven 





On 26/03/14 16:40, "Vinay Kumar Shukla" < vinaykumar.shukla at univr.it > wrote: 

>Hello Everyone! 
> 
>I want to use mrtrix for global tractography. 
>It is possible can any one help me out what would be the 
>step by step process need to follow with DW data sets. 
>looking forward for reply & kind help 
>many thanks in advance 
>cheers !! 
>vinay 
> 
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>Mrtrix-discussion mailing list 
> Mrtrix-discussion at www.nitrc.org 
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